Alignments for a candidate for mcmA in Algoriphagus machipongonensis PR1

GapMind for catabolism of small carbon sources

Alignments for a candidate for mcmA in Algoriphagus machipongonensis PR1

Align methylmalonyl-CoA mutase (EC 5.4.99.2) (characterized)
to candidate WP_008201258.1 ALPR1_RS12840 methylmalonyl-CoA mutase family protein

Query= BRENDA::Q8F222
         (1125 letters)



>NCBI__GCF_000166275.1:WP_008201258.1
          Length = 1125

 Score = 1510 bits (3910), Expect = 0.0
 Identities = 761/1127 (67%), Positives = 917/1127 (81%), Gaps = 12/1127 (1%)

Query: 4    QIYTPKHKVRFITAASLFDGHDASINIMRRILQSSGVEVIHLGHNRSVREIVECAIQEDA 63
            + Y PK+ +R +TAASLFDGHDA+INIMRRI+QS+G EVIHLGHNRSV+EIV+CAIQED 
Sbjct: 6    ETYKPKNHIRIVTAASLFDGHDAAINIMRRIIQSTGCEVIHLGHNRSVQEIVDCAIQEDV 65

Query: 64   QGIAITSYQGGHVEYFKYMIDLLKEKGAGHIKVFGGGGGTILPSEIKELESYGVTRIYSP 123
            Q IAITSYQGGHVE+FKYM DLL EKGAGHIK+FGGGGGTIL  EIKEL  YG++RIYSP
Sbjct: 66   QAIAITSYQGGHVEFFKYMYDLLHEKGAGHIKIFGGGGGTILTEEIKELHDYGISRIYSP 125

Query: 124  DDGRELGLQGMINDLIRRSDFIPPITFNGTLHSSLKDKNPLAIAQMITLVENTFEREDLE 183
            DDGR +GLQGMINDL+ ++D+     F      +L  +N   IA+ I+  EN     D  
Sbjct: 126  DDGRSMGLQGMINDLVSQADYSIGDEFQEGF--TLNKENKGFIARAISAFENY---PDQS 180

Query: 184  KSTLNEKLNFPPGTKSVPVLGITGTGGAGKSSLTDELVRRFLIDFPNKTIAILSVDPSKR 243
               LNE +       ++PVLGITGTGGAGKSSL DELVRRFLIDF +K++AI+SVDPSKR
Sbjct: 181  TDLLNE-VREKSKKSTIPVLGITGTGGAGKSSLVDELVRRFLIDFEDKSLAIISVDPSKR 239

Query: 244  KTGGALLGDRIRMNSISHDRVYMRSFATREANIALNKNVKRSIEVLKSAGFDLIIVETAG 303
            KTGGALLGDRIRMNSI H RV+MRS ATR++N+AL+K V+ +++ +K+AGFD++I+ET+G
Sbjct: 240  KTGGALLGDRIRMNSIHHPRVFMRSLATRQSNLALSKYVQDAVDTVKAAGFDMVILETSG 299

Query: 304  IGQSDSEITEVADVALYVMTPEYGAATQLEKIDMIDYADLIAINKFDKRGALDALRDVKK 363
            IGQSD+EI E +D++LYVMTPEYGAA+QLEKIDM+D+AD+IA+NKFDKRGA DALRDVKK
Sbjct: 300  IGQSDTEIIEHSDLSLYVMTPEYGAASQLEKIDMLDFADVIALNKFDKRGAQDALRDVKK 359

Query: 364  QFQRSRQLFDQNIDLMPVFGTIASQFNDPGTNLLYGNVIRFLSNKLNLDWSSSYEKEEGA 423
            QF+R+  L++   + +PV+GTIASQFNDPG N LY  +I  +  + + +W SS+E   G 
Sbjct: 360  QFKRNHLLWETPDEEIPVYGTIASQFNDPGMNHLYRALISKVG-ETHEEWKSSFELTGGT 418

Query: 424  SEKIFIIPPDRVRYLAEIREECGRYDQFTKNESDKARKLFQLSGAIEVLKS---SGQDIS 480
            SEKI+IIPP R RYL+EI E    YD + + + D A+KL+ +  ++E ++S   + QD  
Sbjct: 419  SEKIYIIPPSRTRYLSEIAETNRNYDVWVEEQKDIAQKLYSIKKSMEAVQSLEVNDQDRL 478

Query: 481  ILKLE--YSKIENSLSLETKKILSSWEEKLKNYQGENFTYKVRDKEIKVSNTTVSLSNLK 538
            + +L   Y ++E  L  + KK +  W E++  Y  + + +KVRDKEIKV     SLS  K
Sbjct: 479  LKELAGVYEQVELELDPKNKKWIEEWPEEVARYSEDFYVFKVRDKEIKVKTYHNSLSETK 538

Query: 539  IPKVAVPKFKDWGEIVRWSFQENFPGEFPFTSGVFPFKRTGEDPTRMFAGEGGPERTNAR 598
            IPK+A+PK++ WG++++W  +EN PG+FP+T+GVFPFKR GEDPTRMFAGEG PERTN R
Sbjct: 539  IPKIALPKYEAWGDLLKWGLRENVPGKFPYTAGVFPFKREGEDPTRMFAGEGSPERTNKR 598

Query: 599  FHYVSLGMPAQRLSTAFDSVTLYGEDPGERPDIYGKIGNSGVSIATLDDAKKLYSGFDLC 658
            FHYVS  MPA+RLSTAFDSVTLYGEDP  RPDIYGKIGNSGV++  LDDAKKLYSGF+L 
Sbjct: 599  FHYVSQDMPAKRLSTAFDSVTLYGEDPDYRPDIYGKIGNSGVNVCCLDDAKKLYSGFNLV 658

Query: 659  NPTTSVSMTINGPAPMVLAFFMNTAIDQACEKHILASGIEKSVRQKIESIYKEKKFPIPK 718
            +P TSVSMTINGPA  + AFFMN AIDQ CE +I   G+EK V  KIE I+K K  P P 
Sbjct: 659  DPLTSVSMTINGPAATMTAFFMNAAIDQQCEVYIKEQGLEKEVDAKIERIFKGKGIPRPV 718

Query: 719  YNTQIPEGNDGLGLMLLGVTGDEVLEKEVYEKIKQETLKLVRGTVQADILKEDQAQNTCI 778
            YN +IP GNDGLGLMLLGV+GD+VL KEVYEKIK ET+  VRGTVQADILKEDQAQNTCI
Sbjct: 719  YNGKIPAGNDGLGLMLLGVSGDQVLPKEVYEKIKAETVSRVRGTVQADILKEDQAQNTCI 778

Query: 779  FSTEFALKMMGDIQEFFIKNQVRNFYSVSISGYHIAEAGANPITQVAFTLANGLTYVEYF 838
            FSTEF+L++MGD+Q++FI + +RNFYSVSISGYHIAEAGANPITQ+A TL+NG TYVEY+
Sbjct: 779  FSTEFSLRLMGDVQDYFIDHGIRNFYSVSISGYHIAEAGANPITQLALTLSNGFTYVEYY 838

Query: 839  LSRGMKIDDFAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMKYKYGANDRSAMLKYHIQT 898
            +SRGM I+ FAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMK KYGAN+RS MLKYHIQT
Sbjct: 839  VSRGMDINKFAPNLSFFFSNGIDPEYAVIGRVARRIWAKAMKLKYGANERSQMLKYHIQT 898

Query: 899  SGRSLHAQEIAFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEESVRRAMAIQLIIN 958
            SGRSLHAQEI FNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTE SVRRAMAIQLIIN
Sbjct: 899  SGRSLHAQEIDFNDIRTTLQALYAIYDNCNSLHTNAYDEAITTPTEASVRRAMAIQLIIN 958

Query: 959  RELGLSKNENPSQGSFIIEELTDLVEQAILEEFHKISERGGVLGAMEMMYQRNKIQEESL 1018
            +ELGLSKNENP QG+FIIEELTDLVE+AI  EF +I+ERGGVLGAME MYQR KIQEES+
Sbjct: 959  KELGLSKNENPLQGAFIIEELTDLVEEAIYLEFDRITERGGVLGAMETMYQRGKIQEESM 1018

Query: 1019 YYESLKHNGEFPVIGVNTFLSKEGSPTIVPQEVIRSTDEEKQAQISALREFHKRNEKDIE 1078
            +YE LKH GE+P+IGVNTFLS EGSPT+ P EVIR+T+EEK++QI  L+  ++ + + + 
Sbjct: 1019 HYEMLKHTGEYPIIGVNTFLSSEGSPTVTPGEVIRATEEEKESQIQTLKNLNQFDPELVS 1078

Query: 1079 NRLRKLKSVSLSNGNIFQELMETSKKVSLGQMTHALYEVGGQYRRSM 1125
              L+ LK +++ NGNIF ELME SK  SLG++THALYEVGGQYRR+M
Sbjct: 1079 THLQNLKKIAVENGNIFSELMEASKHCSLGEITHALYEVGGQYRRNM 1125


Lambda     K      H
   0.317    0.135    0.379 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 3291
Number of extensions: 144
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 1125
Length of database: 1125
Length adjustment: 46
Effective length of query: 1079
Effective length of database: 1079
Effective search space:  1164241
Effective search space used:  1164241
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 58 (26.9 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources